Data from: Morphological and genomic comparisons of Hawaiian and Japanese Black-footed Albatrosses (Phoebastria nigripes) using double digest RADseq: implications for conservation

Evaluating the genetic and demographic independence of populations of threatened species is important for determining appropriate conservation measures, but different technologies can yield different conclusions. Despite multiple studies, the taxonomic status and extent of gene flow between the main breeding populations of Black-footed Albatross (Phoebastria nigripes), a Near-Threatened philopatric seabird, are still controversial. Here, we employ double digest RADseq to quantify the extent of genomewide divergence and gene flow in this species. Our genomewide data set of 9760 loci containing 3455 single nucleotide polymorphisms yielded estimates of genetic diversity and gene flow that were generally robust across seven different filtering and sampling protocols and suggest a low level of genomic variation (θ per site = ~0.00002–0.00028), with estimates of effective population size (Ne = ~500–15 881) falling far below current census size. Genetic differentiation was small but detectable between Japan and Hawaii (FST ≈ 0.038–0.049), with no FST outliers. Additionally, using museum specimens, we found that effect sizes of morphological differences by sex or population rarely exceeded 4%. These patterns suggest that the Hawaiian and Japanese populations exhibit small but significant differences and should be considered separate management units, although the evolutionary and adaptive consequences of this differentiation remain to be identified.评估受威胁物种种群的遗传与种群统计学独立性，对于制定合理的保护措施至关重要，但不同的技术手段可能得出迥异的结论。尽管已有多项相关研究，作为近危（Near-Threatened）的恋巢性海鸟，黑脚信天翁（Phoebastria nigripes）的主要繁殖种群间的分类地位与基因交流程度，仍存在争议。本研究采用双酶切RAD测序（double digest RADseq）技术，对该物种全基因组范围内的分化水平与基因流程度进行量化分析。我们构建的全基因组数据集包含9760个基因座，共涵盖3455个单核苷酸多态性位点（single nucleotide polymorphisms）；经7种不同的过滤与采样方案验证，该数据集得到的遗传多样性与基因流估计结果整体稳健，显示该物种的基因组变异水平较低（每位点θ≈0.00002~0.00028），有效种群大小（Ne≈500~15881）的估计值远低于当前的普查种群数量。日本与夏威夷种群间的遗传分化程度较低但可被检测到（固定指数FST≈0.038~0.049），且未出现FST异常位点。此外，通过对博物馆标本的分析，我们发现不同性别或种群间的形态差异效应量仅极少超过4%。上述结果表明，夏威夷与日本种群虽差异微小但确实存在显著分化，应被视为独立的管理单元；不过该分化所带来的进化与适应性后果仍有待进一步阐明。